Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009992.1 Kokia drynarioides strain JFW-HI SEQ_124747, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 34544
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Found at i:1095 original size:25 final size:24
Alignment explanation
Indices: 1058--1275 Score: 148
Period size: 23 Copynumber: 9.4 Consensus size: 24
1048 ACACTAGCGC
1058 GCTCTCTGT-TTAGCAC-GTCTCGT
1 GCTCTCTGTATTAGCACTGTCT-GT
*
1081 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG-TATTAGCACTGTCTGT
* *
1106 GCTCTCTG-ATTAGCACTTTGTGT
1 GCTCTCTGTATTAGCACTGTCTGT
* * * *
1129 GCTCTTTG-ATTAGTACTTTGTGT
1 GCTCTCTGTATTAGCACTGTCTGT
* * *
1152 ACTCTCTGT-TTAGTACTGTGTGT
1 GCTCTCTGTATTAGCACTGTCTGT
* *
1175 GCTCTCT-TATTAGCACTTTGTGT
1 GCTCTCTGTATTAGCACTGTCTGT
* * * *
1198 GCTCTTTG-ATTAGTACTTTGTGT
1 GCTCTCTGTATTAGCACTGTCTGT
* * * *
1221 GCTCTTTG-ATTAGTACTTTGTGT
1 GCTCTCTGTATTAGCACTGTCTGT
* * *
1244 ACTCTCTGT-TTAGTACTGTGTGT
1 GCTCTCTGTATTAGCACTGTCTGT
1267 GCTCTCTGT
1 GCTCTCTGT
1276 TGCCCAGCAT
Statistics
Matches: 172, Mismatches: 16, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
22 1 0.01
23 150 0.87
24 1 0.01
25 17 0.10
26 3 0.02
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (24 bp):
GCTCTCTGTATTAGCACTGTCTGT
Found at i:1158 original size:46 final size:46
Alignment explanation
Indices: 1091--1271 Score: 247
Period size: 46 Copynumber: 3.9 Consensus size: 46
1081 GCTCTCTGTT
* * * *
1091 ATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCTTTG
1 ATTAGCACTTTGTGTACTCTCTGATTAGTACTGTGTGTGCTCTTTG
* *
1137 ATTAGTACTTTGTGTACTCTCTGTTTAGTACTGTGTGTGCTCTCTT-
1 ATTAGCACTTTGTGTACTCTCTGATTAGTACTGTGTGTGCTCT-TTG
* * *
1183 ATTAGCACTTTGTGTGCTCTTTGATTAGTACTTTGTGTGCTCTTTG
1 ATTAGCACTTTGTGTACTCTCTGATTAGTACTGTGTGTGCTCTTTG
* *
1229 ATTAGTACTTTGTGTACTCTCTGTTTAGTACTGTGTGTGCTCT
1 ATTAGCACTTTGTGTACTCTCTGATTAGTACTGTGTGTGCTCT
1272 CTGTTGCCCA
Statistics
Matches: 117, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
45 2 0.02
46 113 0.97
47 2 0.02
ACGTcount: A:0.13, C:0.17, G:0.22, T:0.48
Consensus pattern (46 bp):
ATTAGCACTTTGTGTACTCTCTGATTAGTACTGTGTGTGCTCTTTG
Found at i:1187 original size:69 final size:69
Alignment explanation
Indices: 1082--1271 Score: 265
Period size: 69 Copynumber: 2.7 Consensus size: 69
1072 ACGTCTCGTG
* *
1082 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCTTTGATTAGTACTT
1 CTCTCTG-T-TTAGTACTGTGTGTGCTCTCTTATTAGCACTTTGTGTGCTCTTTGATTAGTACTT
1147 TGTGTA
64 TGTGTA
1153 CTCTCTGTTTAGTACTGTGTGTGCTCTCTTATTAGCACTTTGTGTGCTCTTTGATTAGTACTTTG
1 CTCTCTGTTTAGTACTGTGTGTGCTCTCTTATTAGCACTTTGTGTGCTCTTTGATTAGTACTTTG
*
1218 TGTG
66 TGTA
* * * * * *
1222 CTCTTTGATTAGTACTTTGTGTACTCTCTGT-TTAGTACTGTGTGTGCTCT
1 CTCTCTGTTTAGTACTGTGTGTGCTCTCT-TATTAGCACTTTGTGTGCTCT
1272 CTGTTGCCCA
Statistics
Matches: 109, Mismatches: 9, Indels: 4
0.89 0.07 0.03
Matches are distributed among these distances:
69 100 0.92
70 2 0.02
71 7 0.06
ACGTcount: A:0.13, C:0.18, G:0.21, T:0.48
Consensus pattern (69 bp):
CTCTCTGTTTAGTACTGTGTGTGCTCTCTTATTAGCACTTTGTGTGCTCTTTGATTAGTACTTTG
TGTA
Found at i:2834 original size:19 final size:20
Alignment explanation
Indices: 2810--2847 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
2800 GATAACATAT
*
2810 ATATTTTTTTAT-TTTTTAA
1 ATATTTTATTATATTTTTAA
2829 ATATTTTATTATATTTTTA
1 ATATTTTATTATATTTTTA
2848 TAAGATGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (20 bp):
ATATTTTATTATATTTTTAA
Found at i:6770 original size:5 final size:5
Alignment explanation
Indices: 6756--6790 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
6746 GTTGAAAATT
*
6756 GAAAA AAAAA GAAAA GAAAA GAAAA GAAAA GAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA
6791 TCAAAATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:10099 original size:17 final size:18
Alignment explanation
Indices: 10074--10120 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
10064 AGGTGATTGT
* *
10074 ATATAAAATTTTA-ATAA
1 ATATTAAATTTAAGATAA
*
10091 ATATTAAATTAAAGATAA
1 ATATTAAATTTAAGATAA
10109 AT-TTAAATTTAA
1 ATATTAAATTTAA
10121 AAAAAAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 19 0.76
18 6 0.24
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
ATATTAAATTTAAGATAA
Found at i:17011 original size:11 final size:10
Alignment explanation
Indices: 16986--17012 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
16976 TTTTATGTTG
16986 TAAAAATTTA
1 TAAAAATTTA
16996 TAAAAATTTA
1 TAAAAATTTA
17006 TAAAAAT
1 TAAAAAT
17013 AATTAATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
TAAAAATTTA
Found at i:17640 original size:31 final size:31
Alignment explanation
Indices: 17599--17667 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
17589 GTGATTTATG
*
17599 ATTGAGCTATTTC-AAAGTTTTCATTGAAGTC
1 ATTGAACTA-TTCAAAAGTTTTCATTGAAGTC
* *
17630 ATTGAACTATTCAAAAGTTTTTATTTAAGTC
1 ATTGAACTATTCAAAAGTTTTCATTGAAGTC
17661 ATTGAAC
1 ATTGAAC
17668 CGTCAATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 3 0.09
31 31 0.91
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (31 bp):
ATTGAACTATTCAAAAGTTTTCATTGAAGTC
Found at i:18265 original size:2 final size:2
Alignment explanation
Indices: 18258--18283 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
18248 TATTCTGGTA
18258 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
18284 TTAAGAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19661 original size:31 final size:29
Alignment explanation
Indices: 19625--19691 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 29
19615 AATTAGTAAA
19625 GATAAAATTTCACTTTAACTCCCCTTAAAAAT
1 GATAAAATTTCA-TTTAA-T-CCCTTAAAAAT
* *
19657 -ATAAAAATTTGATTTAATCCTTTAAAAAT
1 GAT-AAAATTTCATTTAATCCCTTAAAAAT
19686 GATAAA
1 GATAAA
19692 GATATAGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
29 13 0.42
30 3 0.10
31 7 0.23
32 8 0.26
ACGTcount: A:0.46, C:0.13, G:0.04, T:0.36
Consensus pattern (29 bp):
GATAAAATTTCATTTAATCCCTTAAAAAT
Found at i:24376 original size:3 final size:3
Alignment explanation
Indices: 24368--24402 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
24358 TTCAATCTAC
24368 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
24403 ATTTGAATCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:26014 original size:20 final size:21
Alignment explanation
Indices: 25982--26021 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
25972 AAACTAAAAA
25982 ATAAAATATAAATATATAGTT
1 ATAAAATATAAATATATAGTT
*
26003 ATAAAA-ATAAATATGTAGT
1 ATAAAATATAAATATATAGT
26022 AACTACCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.35
Consensus pattern (21 bp):
ATAAAATATAAATATATAGTT
Done.